A mass spectrometric investigation was made of the fragmentation of protonated peptide ions produced by matrix-assisted laser desorption/ionization (MALDI) in an ion source external to a quadrupole ion trap mass analyzer. Highly preferential cleavage was detected at peptide bonds adjacent to aspartic acid residues, as previously observed in a reflecting time-of-flight mass analyzer. In addition, preferential fragmentation was observed, for the first time, adjacent to glutamic acid residues. It is hypothesized that the long time-window of the present measurement (10 4 - 10-1 sec) favors the observation of low-energy, entropically-disfavored reactions at acidic residues. The preferential fragmentation at Asp and Glu residues observed in the ion trap MS has important practical implications. A paper describing these findings has been published in J. Am. Chem. Soc. 117, 5411-5412 (1995). These findings are turning out to have enormous practical application for rapid, confident identification of proteins using our newly developed MALDI ion trap mass spectrometer,as reported in our recent publication (Qin et a], Anal. Chem. 69, (1997) 3995-400 1) and evident from our ongoing efforts to define the total protein composition of the yeast nuclear pore complex (with Blobel and Rout, see elsewhere in this report) .